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as1_main.py
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#!/usr/bin/python
#print cwd
import os
cwd=os.getcwd()
cwd = cwd + '/'
f1= open(cwd +'as1_script.py',"w+")
f2=open(cwd +'as1_temp_script.py',"r")
f4= open(cwd + 'as1_script_gl.py',"w+")
f5= open(cwd + 'no_ligand',"w+")
inf_t=[]
inp= open(cwd +'inputfile.txt',"r")
with inp as ins:
ins = [line.rstrip('\n') for line in ins]
for line in ins:
inf_t=line
inf_t2=inf_t.rstrip('.pdb')
inp.close()
ar=[]
data=[]
ar=f2.read()
flag_inputfile=0
if os.path.isfile("inputfile.pdb"):
flag_inputfile=1
if(flag_inputfile==1):
gl_input="inputfile.pdb"
if(flag_inputfile==0):
gl_input=inf_t
#print gl_input
f1.write('\nimport pymol \nfrom pymol import stored\nfrom pymol import cmd, CmdException\nimport export_to_gl as glmol\ncmd=pymol.cmd\ninput_file=\'%s\'\ncmd.load( input_file , \'%s\' )\nmodelName=\'%s\'\n'%(inf_t,inf_t2,inf_t2))
f4.write('#!/usr/bin/python\nimport os\ncwd=os.getcwd()\ncwd = cwd + \'/\'\nimport pymol \nfrom pymol import stored\nfrom pymol import cmd, CmdException\nimport os \nimport export_to_gl as glmol\ncmd=pymol.cmd\ninput_file=\'%s\'\ncmd.load( cwd + input_file , \'inputfile\' )\nmodelName=\'inputfile\'\n'%gl_input)
input_file ='Active_site1'
f3= open(cwd + input_file,"r")
data=f3.readlines()
k=0
#print data[1]
k=len(data)
f5.write('%s'%(k-1))
f_metal= open('metal_1',"r")
#print k
if(k==1):
f1.write('lig_data=[]')
f4.write('lig_data=[]')
if(k>1):
f1.write('lig_data=[')
f4.write('lig_data=[')
#f1.write(data)
t=0;
for i in data:
f1.write('\'')
f4.write('\'')
i=i.rstrip('\n')
f1.write(str(i))
f4.write(str(i))
if (t<k-1):
f1.write('\',')
f4.write('\',')
t=t+1
f1.write('\']\n')
f4.write('\']\n')
metal_data=[]
metal_data_t=f_metal.readlines()
for i in metal_data_t:
i=i.rstrip('\n')
if (i!=''):
metal_data.append(i)
f1.write('metals=[')
f4.write('metals=[')
#f1.write(data)
t_m=0;
k_m=len(metal_data)-1
#print metal_data
if (k_m==0):
print 'nometals'
f1.write(']\n')
f4.write(']\n')
if (k_m>0):
for i in metal_data[1:]:
f1.write('\'')
f4.write('\'')
i=i.rstrip('\n')
if (i!=''):
f1.write(str(i))
f4.write(str(i))
if (t_m<k_m-1):
f1.write('\',')
f4.write('\',')
t_m=t_m+1
f1.write('\']\n')
f4.write('\']\n')
f1.write(ar)
f4.write(ar)
f1.write("\nout_atoms()")
sst = 'as1_glmol_sst.png'
impf = 'as1_glmol.html'
f4.write('\ndef t_run():\n\tinput_file=\'%s\'\n\tmodelName=\'inputfile\'\n\tcmd.load( cwd + input_file , \'inputfile\')\n\tout_atoms()\n\tglmol.dump_rep(modelName, \'%s\', \'%s\')\n\tpymol.cmd.quit()\nt_run()\n'%(gl_input,sst,impf))
f4.close()
f1.close()
f2.close()
f3.close()
f_metal.close()